Comment 3 for bug 720758

This looks like just a matter of what the default set of word selection characters is.

CODE:

In src/settings.c line 124 we find:

  setting->word_selection_characters = g_strdup("-A-Za-z0-9,./?%&#:_");

Adding a ~ to the end of this string changes the default to include ~ .

WORKAROUND:

Users can change this preference themselves, by clicking on
Edit -> Preferences and then on the Advanced tab, and then typing ~ as the last character in the "Select-by-word characters" field and then clicking the "OK" button.

This setting is remembered across reboots, so a user would only need to do this once to have the ~ always included in double-clicked selections in future.